In nbstripout I also made the following changes, though this probably depends on individual taste. Cell toggling isn't reset by clearing output in the notebook GUI, so toggle states may get versioned even if no output is present. Popping prompt_number matches notebook gui behavior (in IPython 2.4.1).

if 'prompt_number' in cell:
cell.pop('prompt_number')
if 'collapsed' in cell:
cell['collapsed'] = False